BN1644 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 3 8.8033e-07 1.1886e-04
Layer 4 3.5128e-06 1.4028e-04
Layer 2 7.1393e-06 4.3837e-02
Layer 5 1.1116e-05 2.6070e-04
Layer 6 2.7746e-04 2.1218e-03
Layer 1 8.2009e-01 7.0391e-01
WM 8.2768e-01 5.7026e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
ATP1A1 Expression Distribution
Gene Specificity Score (GSS)
ATP1A1 GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
ATP1A1 Layer 4 2.5195 0.8099
SULT4A1 Layer 5 2.7012 0.8096
TUBB3 Layer 5 2.6133 0.8045
SERPINI1 Layer 4 2.7715 0.8040
NAP1L2 Layer 4 2.8086 0.8029
GABRA1 Layer 4 2.6016 0.8008
SH3GL2 Layer 5 2.7246 0.7996
SV2A Layer 4 2.7422 0.7995
MGST3 Layer 5 2.5273 0.7993
MORF4L2 Layer 4 2.7070 0.7991
CPLX1 Layer 5 2.7305 0.7990
GLS Layer 5 2.4785 0.7957
GHITM Layer 5 2.5449 0.7956
RAB3A Layer 5 2.6426 0.7956
HPCA Layer 4 2.9307 0.7950
NDRG4 Layer 5 2.6484 0.7950
CAMK2G Layer 5 2.6719 0.7945
GNB1 Layer 5 2.3809 0.7941
MDH1 Layer 4 2.5957 0.7939
SYT4 Layer 5 2.5664 0.7927
CEND1 Layer 3 2.5781 0.7927
PINK1 Layer 5 2.3086 0.7922
VDAC1 Layer 5 2.4727 0.7918
TMEM130 Layer 5 2.5215 0.7908
CHGA Layer 4 2.6279 0.7907
APBB1 Layer 4 2.3916 0.7900
APLP2 Layer 4 2.5566 0.7900
MTCH1 Layer 5 2.3652 0.7896
ATP6V0B Layer 5 2.4727 0.7894
SYP Layer 5 2.5391 0.7881
SNCA Layer 5 2.5332 0.7879
DCLK1 Layer 5 2.6133 0.7873
PRKAR1B Layer 5 2.5957 0.7863
NAPA Layer 4 2.4570 0.7862
TOLLIP Layer 4 2.5508 0.7861
OAZ1 Layer 5 2.3184 0.7860
AARS Layer 5 2.3555 0.7855
CLTB Layer 5 2.4395 0.7837
RAB3C Layer 5 2.5605 0.7829
HSPA9 Layer 4 2.4785 0.7823
INPP5F Layer 3 2.6602 0.7816
GABRG2 Layer 4 2.6543 0.7809
DNAJC6 Layer 4 2.3867 0.7807
TLE5 Layer 5 2.3398 0.7803
ATP1A3 Layer 5 2.6367 0.7800
COX7B Layer 5 2.5566 0.7800
PFKP Layer 5 2.7656 0.7796
SNAP91 Layer 4 2.7363 0.7795
ATP5F1A Layer 5 2.4453 0.7795
YWHAH Layer 5 2.3398 0.7792

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1644
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1644_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1644/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1644/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1644/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1644/report/PD/BN1644_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1644/report/PD/BN1644_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:40:59
  • Number of Processes: 10
  • Spending Time: 0h 3m